‡We describe the use of singular value decomposition in transforming genome-wide expression data from genes 3 arrays space to reduced diagonalized ‘‘eigengenes’’ 3 ‘‘eigenarrays’’ space, where the eigengenes (or eigenarrays) are unique orthonormal superpositions of the genes (or arrays). Normalizing the data by filtering out the eigengenes (and eigenarrays) that are inferred to represent noise or experimental artifacts enables meaningful comparison of the expression of different genes across different arrays in different experiments. Sorting the data according to the eigengenes and eigenarrays gives a global picture of the dynamics of gene expression, in which individual genes and arrays appear to be classified into groups of similar regulation and function, or similar cellular state and biological phenotype, respectively. After normalization and sorting, the significant eigengenes and eigenarrays can be associated with observed genome-wide effects of regulators, or with measured samples, in which these regulators are overactive or underactive, respectively.

Singular Value Decomposition for Genome-Wide Expression Data Processing and Modeling

Matrix Differential Calculus with Applications in Statistics and Econometrics

Random walks are ubiquitous in the sciences, and they are interesting from both theoretical and practical perspectives. They are one of the most fundamental types of stochastic processes; can be used to model numerous phenomena, including diffusion, interactions, and opinions among humans and animals; and can be used to extract information about important entities or dense groups of entities in a network. Random walks have been studied for many decades on both regular lattices and (especially in the last couple of decades) on networks with a variety of structures. In the present article, we survey the theory and applications of random walks on networks, restricting ourselves to simple cases of single and non-adaptive random walkers. We distinguish three main types of random walks: discrete-time random walks, node-centric continuous-time random walks, and edge-centric continuous-time random walks. We first briefly survey random walks on a line, and then we consider random walks on various types of networks. We extensively discuss applications of random walks, including ranking of nodes (e.g., PageRank), community detection, respondent-driven sampling, and opinion models such as voter models.

Random walks and diffusion on networks

https://research-information.bris.ac.uk/files/125866845/Full_text_PDF_accepted_author_manuscript_.pdf

Tutorial presented at High Performance Computing Center, Stuttgart. 1 July 2005, Stuttgart, Germany.

Introduction to computational biology

In this paper, we propose and develop an iterative method to calculate a limiting probability distribution vector of a transition probability tensor arising from a higher order Markov chain. In the model, the computation of such limiting probability distribution vector can be formulated as a -eigenvalue problem associated with the eigenvalue 1 of where all the entries of are required to be non-negative and its summation must be equal to one. This is an analog of the matrix case for a limiting probability vector of a transition probability matrix arising from the first-order Markov chain. We show that if is a transition probability tensor, then solutions of this -eigenvalue problem exist. When is irreducible, all the entries of solutions are positie. With some suitable conditions of , the limiting probability distribution vector is even unique. Under the same uniqueness assumption, the linear convergence of the iterative method can be established. Numerical examples are presented to illustrate the ...

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On the limiting probability distribution of a transition probability tensor

A general modulus-based matrix splitting method for linear complementarity problems of H-matrices

Modified Gauss–Seidel type methods and Jacobi type methods for Z-matrices

The tensor splitting with application to solve multi-linear systems

In this paper, we study the global uniqueness and solvability (GUS-property) of tensor complementarity problems (TCPs) for some special structured tensors. The modulus equation for TCPs is also pro...

Wen Li

Papers

On the limiting probability distribution of a transition probability tensor

A general modulus-based matrix splitting method for linear complementarity problems of H-matrices

Modified Gauss–Seidel type methods and Jacobi type methods for Z-matrices

The tensor splitting with application to solve multi-linear systems

Tensor complementarity problems: the GUS-property and an algorithm